Taxonomic Refinement of Xanthomonas arboricola

Abstract

Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of non-pathogenic and taxonomically un-validated strains are also designated as X. arboricola leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that out of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine belonging to the core clade of the species regardless of the argue of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola due to the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T, and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. either belonging to previously described species or representing novel species which await formal description.

Reassessment of the occurrence and distribution of Xanthomonas arboricola on fruit trees in Iran

“…populi did not belong to X. arboricola due to the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, Zarei et al (2022) proposed to elevate the two pathovars to the rank of species as X. guizotiae and X. populina, respectively.…”

“…Several nonpathogenic (thus with no pathovar status) strains are also designated as X. arboricola in the literature and public databases (Garita-Cambronero et al, 2018;Vauterin et al, 1995;Zarei et al, 2022). Nonpathogenic strains of X. arboricola have been isolated from host tissues with and without symptoms, that is, walnut buds, sour cherry and peach leaves (Essakhi et al, 2015;Garita-Cambronero et al, 2016a, 2016b.…”

DNA Markers for Detection and Genotyping of Xanthomonas euroxanthea

“…Interestingly, apart from its occurrence in walnuts (Juglans regia), recent evidence was gathered reporting the isolation of X. euroxanthea from distinct plant host species, such as Carya illinoensis (pecan; strains CPBF 761 and CPBF 766), that together with walnut (Juglans regia; strains CPBF 367, CPBF 424 T , CPBF 426 and CFBP 7653) belong to the Juglandaceae family; Solanum lycopersicum (tomato plants; strains BRIP 62409, BRIP 62411, BRIP 62415 and BRIP 62418) a member of the Solanaceae family [7][8][9]; and Phaseolus vulgaris (common bean; strain CFBP 7622, previously misclassified as X. arboricola [10,11]), a Fabaceae plant species.…”

“…More strikingly is that X. arboricola strains were also isolated from all the mentioned plant species, suggesting that both X. euroxanthea and X. arboricola share the same host plants, including the same plant specimen, which raises questions regarding co-colonization and niche-specific adaptations [7,8,12]. Still, taking into consideration the recent taxonomic refinement of X. arboricola species and the unearthing of six new X. euroxanthea strains (2949, 2955, 2957, 2974, 3640 and F2) [11], it is foreseeable the identification of additional X. euroxanthea isolates from plant species that have passed unnoticed so far.…”

“…Altogether, the common ecological niche of these two closely related species, plus their cosmopolitan distribution and co-occurrence in different host plant species resulted in misclassifying some X. euroxanthea isolates as X. arboricola [8,10,11], which calls for the need to develop methods for the detection and genotyping of this bacterial species. Over the years, different diagnostic and molecular typing tools have been developed for a variety of xanthomonads [13], namely for X. arboricola including their most studied pathovars juglandis [14,15] and pruni [16][17][18][19], aiming to address their diversity within a geographic or epidemiological context.…”